This is the second article from NY Times that is slightly biased in favor of the FBI. The first was "Apple's Privacy Fight Tests Relationship With White House" 
From the article,
> denied the United States government's request that Apple extract data from an iPhone
This is oversimplified and a biased viewpoint. Apple has extracted data from phones in the past for the DOJ. This case is different. Apple is being asked to put its stamp of approval on special software that breaks the phone's security features.
> Timothy D. Cook, has refused to comply with a federal court order to help break into the phone, saying that he needs to protect the data of all customers
Oversimplified, again. Apple has filed a long brief detailing many of their objections, including a breach of their first amendment rights, claiming what the FBI is asking is compelled speech. 
> Both the F.B.I. and Apple have called for Congress to step in to help settle the question of when law enforcement should get access to citizens' private data
Apple certainly hasn't called for a new law. No new law is needed to support their position. Cook has said that if a debate needs to take place, it should happen in Congress where the public has a voice. 
> While judges around the country have signed at least 70 orders at the request of the government compelling Apple to access data on phones, this was the first time that a judge and Apple have pushed back.
Again, oversimplifying and muddying the issue. Those other orders were under different circumstances. Apple had direct access to data in those cases, and did not need to create signed software that circumvents their security mechanisms in order to comply.
> During the case, Judge Orenstein said he found it puzzling that Apple had not previously resisted the use of the All Writs Act, including in other cases where Apple had complied with the order.
No mention of Apple's response here. Given Judge Orenstein's 50 page ruling in Apple's favor , one can only imagine that Apple told the Judge they had direct access to data in those cases, but did not have it for the NY drug case, and that the judge later came to understand that answer.
> Ultimately, Judge Orenstein argued that the government couldn't use the All Writs Act to ask Apple to help extract information from a device because that request falls under a different law, the Communications Assistance for Law Enforcement Act, or Calea.
The judge did not say that the request falls under CALEA. Rather, he explicitly stated that CALEA does not apply to Apple in this case over the course of 20 pages . He even says that Congress' omission of a statute in CALEA that would include Apple in this case does not mean that Congress did not consider including such a circumstance, and therefore, Congress intentionally chose not to create such a restriction,
I therefore conclude that what the government seeks here is "to have the court give it authority that Congress chose not to confer." 
> "From a technical, legal standpoint, it doesn't really have much of an effect in the California districts," Mr. Berg said.
I doubt that. It is not binding, but common sense tells you that the San Bernardino magistrate will read the NY drug case's memorandum.
Tim Cook: If there should be a law that compels us to do it, it should be passed out in the open, and the people of America should get a voice in that. The right place for that debate to occur is in Congress.